Roofing Job - Tergniet, WC, 6525

My roof was replaced but have couple places with water leaks when raining. Also the roof ends in some areas are not fully finished as my builder, injured himself and not able to complete. The second important seal is required for the fireplace funnel that is open through the roof but not sealed. It's the last part of the roof that was replaced. Waterproofing or to make sure it's fully covered is what I require. . Thanks.